Starting phenix.real_space_refine on Sun Mar 24 05:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0y_4700/03_2024/6r0y_4700_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 103 5.16 5 C 25034 2.51 5 N 7293 2.21 5 O 7734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ARG 281": "NH1" <-> "NH2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 360": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40169 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3609 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "E" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3618 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3608 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1441 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 26, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 3190 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2628 Unresolved non-hydrogen dihedrals: 1714 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 12, 'TYR:plan': 18, 'ASN:plan1': 7, 'TRP:plan': 12, 'HIS:plan': 21, 'PHE:plan': 33, 'GLU:plan': 56, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.38, per 1000 atoms: 0.51 Number of scatterers: 40169 At special positions: 0 Unit cell: (152.985, 150.815, 254.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 4 15.00 Mg 1 11.99 O 7734 8.00 N 7293 7.00 C 25034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.67 Conformation dependent library (CDL) restraints added in 7.5 seconds 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 36 sheets defined 51.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.73 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 removed outlier: 4.531A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.048A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.239A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 358 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 411 through 414 No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.695A pdb=" N ASP A 436 " --> pdb=" O SER A 433 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.516A pdb=" N ARG A 440 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 5.545A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 509 through 530 Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 556 through 576 Proline residue: A 560 - end of helix removed outlier: 4.632A pdb=" N GLU A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 565 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 567 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 574 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.924A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 298 through 315 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 352 through 364 removed outlier: 4.265A pdb=" N ALA B 355 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 358 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 447 through 470 removed outlier: 4.733A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.728A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 559 through 572 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 259 through 268 removed outlier: 4.679A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 296 through 314 removed outlier: 5.715A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 339 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 470 removed outlier: 5.360A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 481 through 493 Processing helix chain 'C' and resid 509 through 531 removed outlier: 4.984A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 559 through 576 removed outlier: 4.929A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 231 through 247 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.339A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 291 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.520A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 4.057A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 4.340A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 228 through 248 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 285 through 295 removed outlier: 4.264A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 290 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 291 " --> pdb=" O TYR E 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 293 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 341 through 347 Processing helix chain 'E' and resid 361 through 364 Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.855A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE E 392 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 removed outlier: 4.139A pdb=" N ARG E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.177A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 161 through 170 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 228 through 247 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.370A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR F 293 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 373 through 396 removed outlier: 4.590A pdb=" N LYS F 376 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 378 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 382 " --> pdb=" O SER F 379 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 385 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL F 396 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 433 through 445 removed outlier: 4.112A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'G' and resid 8 through 69 removed outlier: 3.676A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 123 through 168 Processing helix chain 'G' and resid 170 through 205 removed outlier: 4.081A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 16 removed outlier: 3.589A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 19 through 100 removed outlier: 4.014A pdb=" N LYS I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 106 No H-bonds generated for 'chain 'I' and resid 104 through 106' Processing helix chain 'I' and resid 108 through 118 Processing helix chain 'J' and resid 3 through 96 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 100 through 113 removed outlier: 4.635A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 132 removed outlier: 3.863A pdb=" N LEU J 128 " --> pdb=" O PRO J 125 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.935A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 105 removed outlier: 3.923A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 3 through 93 removed outlier: 4.020A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.450A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 17 removed outlier: 4.106A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 Processing helix chain 'M' and resid 34 through 41 Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 54 through 73 removed outlier: 4.082A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Proline residue: M 73 - end of helix Processing helix chain 'M' and resid 79 through 85 Processing helix chain 'M' and resid 89 through 105 Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 146 through 156 removed outlier: 4.221A pdb=" N ARG M 156 " --> pdb=" O ARG M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 181 Processing helix chain 'M' and resid 186 through 206 Processing helix chain 'M' and resid 214 through 217 No H-bonds generated for 'chain 'M' and resid 214 through 217' Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 239 through 243 Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.900A pdb=" N GLY M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLN M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 309 Processing helix chain 'N' and resid 14 through 26 Processing helix chain 'N' and resid 47 through 70 Processing helix chain 'N' and resid 84 through 115 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 119 through 128 Processing helix chain 'N' and resid 150 through 159 removed outlier: 5.104A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 197 Processing helix chain 'N' and resid 213 through 268 Proline residue: N 228 - end of helix removed outlier: 5.642A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 296 removed outlier: 3.523A pdb=" N LYS N 287 " --> pdb=" O VAL N 284 " (cutoff:3.500A) Proline residue: N 288 - end of helix removed outlier: 3.520A pdb=" N ALA N 295 " --> pdb=" O GLU N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 335 removed outlier: 4.182A pdb=" N LEU N 332 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 362 removed outlier: 3.520A pdb=" N VAL N 351 " --> pdb=" O THR N 348 " (cutoff:3.500A) Proline residue: N 352 - end of helix removed outlier: 4.991A pdb=" N PHE N 355 " --> pdb=" O PRO N 352 " (cutoff:3.500A) Proline residue: N 356 - end of helix removed outlier: 3.846A pdb=" N GLY N 360 " --> pdb=" O PHE N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 385 Processing helix chain 'N' and resid 400 through 424 removed outlier: 3.685A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 488 Processing helix chain 'N' and resid 492 through 515 Processing helix chain 'N' and resid 525 through 542 Processing helix chain 'N' and resid 548 through 586 removed outlier: 4.511A pdb=" N HIS N 561 " --> pdb=" O HIS N 557 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE N 562 " --> pdb=" O ILE N 558 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE N 564 " --> pdb=" O SER N 560 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 631 removed outlier: 4.611A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.849A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 47 removed outlier: 4.211A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 79 Proline residue: O 62 - end of helix removed outlier: 5.888A pdb=" N LEU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL O 66 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 47 removed outlier: 4.177A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 78 Proline residue: P 62 - end of helix removed outlier: 5.310A pdb=" N LEU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL P 66 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 47 removed outlier: 4.150A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 78 Proline residue: Q 62 - end of helix removed outlier: 5.816A pdb=" N LEU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 47 removed outlier: 3.982A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 4.002A pdb=" N PHE R 52 " --> pdb=" O ARG R 49 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY R 53 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 55 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU R 56 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU R 61 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 3.803A pdb=" N LEU R 65 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 47 removed outlier: 4.227A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 79 removed outlier: 4.870A pdb=" N GLY S 53 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR S 54 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA S 55 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU S 61 " --> pdb=" O PHE S 58 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.571A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 79 Proline residue: T 62 - end of helix removed outlier: 5.702A pdb=" N LEU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 47 removed outlier: 4.056A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 79 Proline residue: U 62 - end of helix removed outlier: 5.892A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 47 removed outlier: 4.117A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 79 Proline residue: V 62 - end of helix removed outlier: 5.901A pdb=" N LEU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 47 removed outlier: 4.087A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 79 removed outlier: 3.610A pdb=" N PHE W 52 " --> pdb=" O ARG W 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY W 53 " --> pdb=" O SER W 50 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR W 54 " --> pdb=" O ASN W 51 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU W 61 " --> pdb=" O PHE W 58 " (cutoff:3.500A) Proline residue: W 62 - end of helix removed outlier: 4.352A pdb=" N LEU W 65 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 47 removed outlier: 3.683A pdb=" N ILE X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 79 Proline residue: X 62 - end of helix removed outlier: 5.929A pdb=" N LEU X 65 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL X 66 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 45 removed outlier: 4.114A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 78 Proline residue: Y 62 - end of helix removed outlier: 6.050A pdb=" N LEU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL Y 66 " --> pdb=" O PRO Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 47 removed outlier: 3.878A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 Processing helix chain 'Z' and resid 64 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 63 through 65 removed outlier: 6.651A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 30 Processing sheet with id= C, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= D, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.978A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N VAL A 320 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.528A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.406A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.514A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.720A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN B 290 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY B 254 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 249 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 255 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.725A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 removed outlier: 4.081A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.740A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= N, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= O, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.815A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 137 through 139 Processing sheet with id= R, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.607A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 18 through 22 removed outlier: 3.635A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= U, first strand: chain 'D' and resid 152 through 154 Processing sheet with id= V, first strand: chain 'D' and resid 217 through 222 removed outlier: 6.266A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 188 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 71 through 76 removed outlier: 3.757A pdb=" N ILE E 32 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU E 22 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE E 11 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= Y, first strand: chain 'E' and resid 90 through 93 removed outlier: 7.211A pdb=" N SER E 217 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE E 93 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 219 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET E 194 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR E 258 " --> pdb=" O MET E 194 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE E 196 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.704A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL F 56 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= AC, first strand: chain 'F' and resid 188 through 192 removed outlier: 4.164A pdb=" N ALA F 188 " --> pdb=" O HIS F 252 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 90 through 96 Processing sheet with id= AE, first strand: chain 'H' and resid 44 through 48 removed outlier: 5.598A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.882A pdb=" N ALA J 123 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA J 123 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLY J 151 " --> pdb=" O ALA J 123 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 141 through 144 Processing sheet with id= AH, first strand: chain 'N' and resid 303 through 306 removed outlier: 4.425A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 140 through 145 Processing sheet with id= AJ, first strand: chain 'N' and resid 389 through 391 2342 hydrogen bonds defined for protein. 6498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.67 Time building geometry restraints manager: 18.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11677 1.33 - 1.45: 6341 1.45 - 1.57: 22492 1.57 - 1.69: 6 1.69 - 1.81: 194 Bond restraints: 40710 Sorted by residual: bond pdb=" C GLY F 16 " pdb=" N PRO F 17 " ideal model delta sigma weight residual 1.331 1.306 0.025 7.90e-03 1.60e+04 1.04e+01 bond pdb=" C ASP F 353 " pdb=" N PRO F 354 " ideal model delta sigma weight residual 1.331 1.310 0.021 7.90e-03 1.60e+04 7.28e+00 bond pdb=" CB ASP D 327 " pdb=" CG ASP D 327 " ideal model delta sigma weight residual 1.516 1.454 0.062 2.50e-02 1.60e+03 6.20e+00 bond pdb=" CA MET D 194 " pdb=" CB MET D 194 " ideal model delta sigma weight residual 1.539 1.426 0.114 4.88e-02 4.20e+02 5.45e+00 bond pdb=" CG1 ILE D 392 " pdb=" CD1 ILE D 392 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.32e+00 ... (remaining 40705 not shown) Histogram of bond angle deviations from ideal: 96.26 - 104.24: 675 104.24 - 112.23: 19785 112.23 - 120.21: 18020 120.21 - 128.20: 16649 128.20 - 136.18: 217 Bond angle restraints: 55346 Sorted by residual: angle pdb=" C THR E 197 " pdb=" N GLN E 198 " pdb=" CA GLN E 198 " ideal model delta sigma weight residual 121.54 133.20 -11.66 1.91e+00 2.74e-01 3.73e+01 angle pdb=" N ILE N 454 " pdb=" CA ILE N 454 " pdb=" C ILE N 454 " ideal model delta sigma weight residual 113.42 106.99 6.43 1.17e+00 7.31e-01 3.02e+01 angle pdb=" C ILE F 106 " pdb=" N THR F 107 " pdb=" CA THR F 107 " ideal model delta sigma weight residual 121.80 134.96 -13.16 2.44e+00 1.68e-01 2.91e+01 angle pdb=" C THR D 258 " pdb=" N ASP D 259 " pdb=" CA ASP D 259 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LYS E 149 " pdb=" N LEU E 150 " pdb=" CA LEU E 150 " ideal model delta sigma weight residual 122.31 110.75 11.56 2.34e+00 1.83e-01 2.44e+01 ... (remaining 55341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 24085 27.88 - 55.75: 378 55.75 - 83.63: 12 83.63 - 111.50: 1 111.50 - 139.38: 2 Dihedral angle restraints: 24478 sinusoidal: 7991 harmonic: 16487 Sorted by residual: dihedral pdb=" CA ASP H 85 " pdb=" C ASP H 85 " pdb=" N VAL H 86 " pdb=" CA VAL H 86 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA ARG E 345 " pdb=" C ARG E 345 " pdb=" N LYS E 346 " pdb=" CA LYS E 346 " ideal model delta harmonic sigma weight residual 180.00 145.66 34.34 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 24475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5793 0.099 - 0.198: 593 0.198 - 0.296: 25 0.296 - 0.395: 4 0.395 - 0.494: 1 Chirality restraints: 6416 Sorted by residual: chirality pdb=" CB ILE C 454 " pdb=" CA ILE C 454 " pdb=" CG1 ILE C 454 " pdb=" CG2 ILE C 454 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE F 106 " pdb=" CA ILE F 106 " pdb=" CG1 ILE F 106 " pdb=" CG2 ILE F 106 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 6413 not shown) Planarity restraints: 7460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 279 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 280 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 311 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO D 312 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 407 " -0.021 2.00e-02 2.50e+03 1.91e-02 9.14e+00 pdb=" CG TRP C 407 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 407 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 407 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 407 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 407 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 407 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 407 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 407 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 407 " -0.001 2.00e-02 2.50e+03 ... (remaining 7457 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2095 2.71 - 3.26: 39600 3.26 - 3.81: 65711 3.81 - 4.35: 75338 4.35 - 4.90: 129948 Nonbonded interactions: 312692 Sorted by model distance: nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 601 " model vdw 2.169 2.170 nonbonded pdb=" O LYS D 149 " pdb=" OG1 THR D 333 " model vdw 2.177 2.440 nonbonded pdb=" OD1 ASP D 34 " pdb=" OG SER D 74 " model vdw 2.231 2.440 nonbonded pdb=" O ARG D 274 " pdb=" O2' ADP D 501 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR C 291 " pdb=" OD1 ASN C 293 " model vdw 2.267 2.440 ... (remaining 312687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 577) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 464) selection = (chain 'E' and resid 5 through 464) selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 2 through 187) } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.440 Check model and map are aligned: 0.550 Set scattering table: 0.300 Process input model: 104.090 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 40710 Z= 0.571 Angle : 1.078 15.832 55346 Z= 0.579 Chirality : 0.060 0.494 6416 Planarity : 0.008 0.092 7460 Dihedral : 10.271 139.381 13942 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.08), residues: 5793 helix: -2.33 (0.06), residues: 3110 sheet: -2.85 (0.18), residues: 585 loop : -3.29 (0.11), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP C 407 HIS 0.016 0.004 HIS E 323 PHE 0.036 0.003 PHE A 269 TYR 0.036 0.003 TYR D 383 ARG 0.019 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1040 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable